Buggy code:
public static int AMPLITUDE_UPPER_THRESHOLD = 2 * 65535 ; public static double MU_THRESHOLD = 0.707 ; public static double SIGMA_RATIO_LOWER_THRESHOLD = 0.67 ; public static double SIGMA_RATIO_UPPER_THRESHOLD = 1.5 ; public static double R_SQUARED_THRESHOLD = 0.5 ; public static boolean FILTER_ON_AMPLITUDE = true ; public static boolean FILTER_ON_MU = true ; public static boolean FILTER_ON_SIGMA = true ; public static boolean FILTER_ON_R_SQUARED = true ; public static int VALID_LINE_POINT_THRESHOLD = 2 ; public static boolean SKELETONIZE_POINTS_MASK = true ; public static boolean FILTER_POINTS_MASK = true ; public static double ANGULAR_RESOLUTION = 6.0 ; public static int ODF_STEPS = ( ( int ) ( 180.0 // ( Trace_Microtubules . ANGULAR_RESOLUTION ) ) ) ; public static double ANISOTROPY_FACTOR = 5 ; public static int ODF_PEAK_WIDTH = 5 ; public static boolean DEBUG_MODE_ENABLED = true ; public static boolean SHOW_RESULTS_TABLE = false ; public static boolean SHOW_VECTOR_OVERLAY = true ; public static boolean SHOW_ODF_OVERLAY = true ; public static boolean USE_VECTOR_NORMALS = true ; public static boolean USE_TRANSPARENCY = true ; public Trace_Microtubules ( ) { } public void run ( String arg ) { ImagePlus imp = IJ . getImage ( ) ; if ( imp == null ) return ; GenericDialog gd = new GenericDialog ( "Trace<seq2seq4repair_space>microtubules" ) ; gd . addNumericField ( "PSF_sigma" , Prefs . get ( "mt_trace.psf_sigma" , Trace_Microtubules . SIGMA ) , 2 ) ; gd . setInsets ( 10 , 20 , 0 ) ; gd . addCheckbox ( "Reduce_noise" , Prefs . get ( "mt_trace.reduce_noise" , Trace_Microtubules . REDUCE_NOISE ) ) ; gd . addCheckbox ( "Suppress_background" , Prefs . get ( "mt_trace.suppress_background" , Trace_Microtubules . SUPPRESS_BACKGROUND ) ) ; gd . setInsets ( 10 , 20 , 0 ) ; gd . addCheckbox ( "Filter_on_amplitude" , Prefs . get ( "mt_trace.filter_amplitude" , true ) ) ; gd . addNumericField ( "Amplitude_lower_threshold" , Prefs . get ( "mt_trace.filter_amplitude_lower_threshold" , Trace_Microtubules . AMPLITUDE_LOWER_THRESHOLD ) , 0 ) ; gd . addNumericField ( "Amplitude_upper_threshold" , Prefs . get ( "mt_trace.filter_amplitude_upper_threshold" , Trace_Microtubules . AMPLITUDE_UPPER_THRESHOLD ) , 0 ) ; gd . addCheckbox ( "Filter_on_mu" , Prefs . get ( "mt_trace.filter_mu" , true ) ) ; gd . addNumericField ( "Mu_absolute_threshold" , Prefs . get ( "mt_trace.filter_mu_threshold" , Trace_Microtubules . MU_THRESHOLD ) , 3 ) ; gd . addCheckbox ( "Filter_on_sigma" , Prefs . get ( "mt_trace.filter_sigma" , true ) ) ; gd . addNumericField ( "Sigma_ratio_lower_threshold" , Prefs . get ( "mt_trace.filter_sigma_lower_threshold" , Trace_Microtubules . SIGMA_RATIO_LOWER_THRESHOLD ) , 2 ) ; gd . addNumericField ( "Sigma_ratio_upper_threshold" , Prefs . get ( "mt_trace.filter_sigma_upper_threshold" , Trace_Microtubules . SIGMA_RATIO_UPPER_THRESHOLD ) , 2 ) ; gd . addCheckbox ( "Filter_on_R-squared" , Prefs . get ( "mt_trace.filter_r_squared" , true ) ) ; gd . addNumericField ( "R-squared_threshold" , Prefs . get ( "mt_trace.filter_r_squared_threshold" , Trace_Microtubules . R_SQUARED_THRESHOLD ) , 2 ) ; gd . setInsets ( 10 , 20 , 0 ) ; gd . addNumericField ( "Valid_line_point_threshold" , Prefs . get ( "mt_trace.valid_line_point_threshold" , Trace_Microtubules . VALID_LINE_POINT_THRESHOLD ) , 0 ) ; gd . addCheckbox ( "Skeletonize_point_map" , Prefs . get ( "mt_trace.skeletonize_point_mask" , Trace_Microtubules . SKELETONIZE_POINTS_MASK ) ) ; gd . addCheckbox ( "Filter_point_map" , Prefs . get ( "mt_trace.filter_point_mask" , Trace_Microtubules . FILTER_POINTS_MASK ) ) ; gd . setInsets ( 10 , 20 , 0 ) ; gd . addNumericField ( "Angular_resolution" , Prefs . get ( "mt_trace.angular_resolution" , Trace_Microtubules . ANGULAR_RESOLUTION ) , 1 ) ; gd . addNumericField ( "Anisotropy_factor" , Prefs . get ( "mt_trace.anisotropy_factor" , Trace_Microtubules . ANISOTROPY_FACTOR ) , 1 ) ; gd . addNumericField ( "ODF_peak_width" , Prefs . get ( "mt_trace.odf_peak_width" , Trace_Microtubules . ODF_PEAK_WIDTH ) , 0 ) ; gd . setInsets ( 10 , 20 , 0 ) ; gd . addCheckbox ( "Enable_debug_mode" , Prefs . get ( "mt_trace.debug_mode" , Trace_Microtubules . DEBUG_MODE_ENABLED ) ) ; gd . addCheckbox ( "Show_results_table" , Prefs . get ( "mt_trace.show_results_table" , Trace_Microtubules . SHOW_RESULTS_TABLE ) ) ; gd . addCheckbox ( "Show_vector_overlay" , Prefs . get ( "mt_trace.show_vector_overlay" , Trace_Microtubules . SHOW_VECTOR_OVERLAY ) ) ; <START_BUG> gd . addCheckbox ( "Show_ODF_overlay" , Prefs . get ( "mt_trace.show_odf_overlay" , Trace_Microtubules . SHOW_VECTOR_OVERLAY ) ) ; <END_BUG> gd . addCheckbox ( "Use_vector_normals" , Prefs . get ( "mt_trace.use_vector_normals" , Trace_Microtubules . USE_VECTOR_NORMALS ) ) ; gd . addCheckbox ( "Use_transparency" , Prefs . get ( "mt_trace.use_transparency" , Trace_Microtubules . USE_TRANSPARENCY ) ) ; gd . setOKLabel ( "Trace" ) ; gd . showDialog ( ) ; if ( gd . wasCanceled ( ) ) return ; Trace_Microtubules . SIGMA = gd . getNextNumber ( ) ; Trace_Microtubules . REDUCE_NOISE = gd . getNextBoolean ( ) ; Trace_Microtubules . SUPPRESS_BACKGROUND = gd . getNextBoolean ( ) ; Trace_Microtubules . FILTER_ON_AMPLITUDE = gd . getNextBoolean ( ) ; Trace_Microtubules . AMPLITUDE_LOWER_THRESHOLD = ( ( int ) ( gd . getNextNumber ( ) ) ) ; Trace_Microtubules . AMPLITUDE_UPPER_THRESHOLD = ( ( int ) ( gd . getNextNumber ( ) ) ) ; Trace_Microtubules . FILTER_ON_MU = gd . getNextBoolean ( ) ; Trace_Microtubules . MU_THRESHOLD = gd . getNextNumber ( ) ; Trace_Microtubules . FILTER_ON_SIGMA = gd . getNextBoolean ( ) ; Trace_Microtubules . SIGMA_RATIO_LOWER_THRESHOLD = gd . getNextNumber ( ) ; Trace_Microtubules . SIGMA_RATIO_UPPER_THRESHOLD = gd . getNextNumber ( ) ; Trace_Microtubules . FILTER_ON_R_SQUARED = gd . getNextBoolean ( ) ; Trace_Microtubules . R_SQUARED_THRESHOLD = gd . getNextNumber ( ) ; Trace_Microtubules . VALID_LINE_POINT_THRESHOLD = ( ( int ) ( gd . getNextNumber ( ) ) ) ; Trace_Microtubules . SKELETONIZE_POINTS_MASK = gd . getNextBoolean ( ) ; Trace_Microtubules . FILTER_POINTS_MASK = gd . getNextBoolean ( ) ; Trace_Microtubules . ANGULAR_RESOLUTION = gd . getNextNumber ( ) ; Trace_Microtubules . ODF_STEPS = ( ( int ) ( 180.0 // ( Trace_Microtubules . ANGULAR_RESOLUTION ) ) ) ; Trace_Microtubules . ANISOTROPY_FACTOR = gd . getNextNumber ( ) ; Trace_Microtubules . ODF_PEAK_WIDTH = ( ( int ) ( gd . getNextNumber ( ) ) ) ; Trace_Microtubules . DEBUG_MODE_ENABLED = gd . getNextBoolean ( ) ;

Fix:
gd . addCheckbox ( "Show_ODF_overlay" , Prefs . get ( "mt_trace.show_odf_overlay" , Trace_Microtubules . SHOW_ODF_OVERLAY ) ) ;